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Aspergillus flavus is a ubiquitous saprophytic fungus found in soils across the world. The fungus is the major producer of aflatoxin (AF) B1, which is toxic and a potent carcinogen to humans. Aflatoxin B1 (AFB1) is often detected in agricultural crops such as corn, peanut, almond, and pistachio. It is a serious and recurrent problem and causes substantial economic losses. Wickerhamomyces anomalus WRL-076 was identified as an effective biocontrol yeast against A. flavus. In this study, the associated molecular mechanisms of biocontrol were investigated. We found that the expression levels of eight genes, aflR, aflJ, norA, omtA, omtB, pksA, vbs, and ver-1 in the aflatoxin biosynthetic pathway cluster were suppressed. The decreases ranged from several to 10,000 fold in fungal samples co-cultured with W. anomalus. Expression levels of conidiation regulatory genes brlA, abaA, and wetA as well as sclerotial regulatory gene (sclR) were all down regulated. Consistent with the decreased gene expression levels, aflatoxin concentrations in cultural medium were reduced to barely detectable. Furthermore, fungal biomass and conidial number were significantly reduced by 60% and more than 95%, respectively. The results validate the biocontrol efficacy of W. anomalus WRL-076 observed in the field experiments.

Aspergillus flavus is a plant and animal pathogen that also produces the potent carcinogen aflatoxin. Aspergillus oryzae is a closely related species that has been used for centuries in the food fermentation industry and is Generally Regarded As Safe (GRAS). Whole genome sequences for these two fungi are now complete, providing us with the opportunity to examine any genomic differences that may explain the different ecological niches of these two fungi, and perhaps to identify pathogenicity factors in A. flavus. These two fungi are very similar in genome size and number of predicted genes. The estimated genome size (36·8 Mb) and predicted number of genes (12 197) for A. flavus is similar to that of A. oryzae (36·7 Mb and 12 079, respectively). These two fungi have significantly larger genomes than Aspergillus nidulans (30·1) and Aspergillus fumigatus (29·4). The A. flavus and A. oryzae genomes are enriched in genes for secondary metabolism, but do not differ greatly from one another in the predicted number of polyketide synthases, nonribosomal peptide synthases or the number of genes coding for cytochrome P450 enzymes. A micro-scale analysis of the two fungi did show differences in DNA correspondence between the two species and in the number of transposable elements. Each species has approximately 350 unique genes. The high degree of sequence similarity between the two fungi suggests that they may be ecotypes of the same species and that A. oryzae has resulted from the domestication of A. flavus.

Corn is one of the most widely grown crops throughout the world. However, many corn fields develop pest problems such as corn borers every year that seriously affect its yield and quality. Corn′s response to initial insect damage involves a variety of changes to the levels of defensive enzymes, toxins, and communicative volatiles. Such a dramatic change secondary metabolism necessitates the regulation of gene expression at the transcript level. In this paper, we summarized the datasets of the transcriptome of corn plants in response to corn stalk borers (Ostrinia furnacalis) and/or methyl jasmonate (MeJA). Altogether, 39, 636 genes were found to be differentially expressed. The sequencing data are available in the NCBI SRA database under accession number SRS965087. Our dataset will provide more scientific and valuable information for future work such as the study of the functions of important genes or proteins and develop new insect-resistant maize varieties. Keywords: RNA-seq, Asian corn borer, jasmonic acid

Aspergillus flavus is a ubiquitous saprophytic fungus found in soils across the world. The fungus is the major producer of aflatoxin (AF) B1, which is toxic and a potent carcinogen to humans. Aflatoxin B1 (AFB1) is often detected in agricultural crops such as corn, peanut, almond, and pistachio. It is a serious and recurrent problem and causes substantial economic losses. Wickerhamomyces anomalus WRL-076 was identified as an effective biocontrol yeast against A. flavus. In this study, the associated molecular mechanisms of biocontrol were investigated. We found that the expression levels of eight genes, aflR, aflJ, norA, omtA, omtB, pksA, vbs, and ver-1 in the aflatoxin biosynthetic pathway cluster were suppressed. The decreases ranged from several to 10,000 fold in fungal samples co-cultured with W. anomalus. Expression levels of conidiation regulatory genes brlA, abaA, and wetA as well as sclerotial regulatory gene (sclR) were all down regulated. Consistent with the decreased gene expression levels, aflatoxin concentrations in cultural medium were reduced to barely detectable. Furthermore, fungal biomass and conidial number were significantly reduced by 60% and more than 95%, respectively. The results validate the biocontrol efficacy of W. anomalus WRL-076 observed in the field experiments.

Aflatoxins are toxic secondary metabolites produced by Aspergillus flavus and a few other closely related species of Aspergillus. These highly toxigenic and carcinogenic mycotoxins contaminate global food and feed supplies, posing widespread health risks to humans and domestic animals. Field application of nonaflatoxigenic strains of A. flavus to compete against aflatoxigenic strains has emerged as one of the best management practices for reducing aflatoxins contamination, yielding successful commercial products for corn, cotton seed, and peanuts. In this study, we sequenced the genome and transcriptome of atoxigenic (does not produce aflatoxin or cyclopiazonic acid) A. flavus strain WRRL 1519 isolated from a tree nut orchard to define the genetic characteristics of the strain in relation to aflatoxigenic and other nonaflatoxigenic A. flavus strains. WRRL 1519 strain was similar to other strains in size (38.0 Mb), GC content (47.2%), number of predicted secondary metabolite gene clusters (46), and number of putative proteins (12 121). About 87.4% of the predicted proteome had high shared identity with protein sequences derived from other A. flavus genomes. However, the atoxigenic A. flavus strain WRRL 1519 had deletions, or low shared identity, for many genes in the clusters required for aflatoxins and cyclopiazonic acid (CPA) synthesis. Over half of the aflatoxin synthesis gene cluster was missing, and none of the components of the CPA gene cluster were identified with high sequence similarity. Importantly, the strain appeared to maintain functional sequences of several genes thought to be required for high infectivity. Since the ability to grow on target crop is an important attribute for a successful biocontrol agent, these results indicate that the nonaflatoxigenic A. flavus strain WRRL 1519 would be a good candidate as a biocontrol agent for reducing aflatoxin and CPA accumulation in high-value nut crops.

Aspergillus flavus is a saprophytic fungus that infects corn, peanuts, tree nuts and other agriculturally important crops. Once the crop is infected the fungus has the potential to secrete one or more mycotoxins, the most carcinogenic of which is aflatoxin. Aflatoxin contaminated crops are deemed unfit for human or animal consumption, which results in both food and economic losses. Within A. flavus, two morphotypes exist: the S strains (small sclerotia) and L strains (large sclerotia). Significant morphological and physiological differences exist between the two morphotypes. For example, the S-morphotypes produces sclerotia that are smaller (< 400 μm), greater in quantity, and contain higher concentrations of aflatoxin than the L-morphotypes (>400 μm). The morphotypes also differ in pigmentation, pH homeostasis in culture and the number of spores produced. Here we report the first full genome sequence of an A. flavus S morphotype, strain AF70. We provide a comprehensive comparison of the A. flavus S-morphotype genome sequence with a previously sequenced genome of an L-morphotype strain (NRRL 3357), including an in-depth analysis of secondary metabolic clusters and the identification SNPs within their aflatoxin gene clusters.

Aflatoxins, produced by Aspergillus flavus and Aspergillus parasiticus, are the most toxic fungal secondary metabolites that contaminate agricultural commodities such as peanuts, cotton and maize. Understanding the underlying mechanisms of crop resistance to fungal infection is an important step for plant breeders to develop better and improved crop varieties for safe production of human food and animal feed. Infection studies have identified a resistant (R) peanut line, GT-C20, which is able to decrease aflatoxin contamination. The mycelial growth of A. flavus NRRL3357 on the R peanut line was much lower than that on the susceptible (S) peanut line, Tifrunner. Besides reducing fungal growth, the R line compared to the S line inhibited aflatoxin production completely. Real-time RT-PCR assays of both the R and S lines infected by A. flavus showed that expression of five aflatoxin biosynthetic pathway genes, the aflR regulatory gene and the aflD, aflM, aflP and aflQ structural genes, was not reduced but was significantly delayed on the R line. The results suggested that resistance factors of the R line acted negatively on A. flavus growth and also altered fungal development. The dysfunction in development changed the timing and the pattern of aflatoxin gene expression, which in part rendered A. flavus unable to produce aflatoxins.

Penicillium is a large genus of common molds with over 400 described species; however, identification of individual species is difficult, including for those species that cause postharvest rots. In this study, blue rot fungi from stored apples and pears were isolated from a variety of hosts, locations, and years. Based on morphological and cultural characteristics and partial amplification of the β-tubulin locus, the isolates were provisionally identified as several different species of Penicillium. These isolates were investigated further using a suite of molecular DNA markers and compared to sequences of the ex-type for cognate species in GenBank, and were identified as P. expansum (3 isolates), P. solitum (3 isolates), P. carneum (1 isolate), and P. paneum (1 isolate). Three of the markers we used (ITS, internal transcribed spacer rDNA sequence; benA, β-tubulin; CaM, calmodulin) were suitable for distinguishing most of our isolates from one another at the species level. In contrast, we were unable to amplify RPB2 sequences from four of the isolates. Comparison of our sequences with cognate sequences in GenBank from isolates with the same species names did not always give coherent data, reinforcing earlier studies that have shown large intraspecific variability in many Penicillium species, as well as possible errors in some sequence data deposited in GenBank.

Blue mold is the vernacular name of a common postharvest disease of stored apples, pears, and quince that is caused by several common species of Penicillium. This study reports the draft genome sequence of Penicillium expansum strain R21, which was isolated from a red delicious apple in 2011 in Pennsylvania.

Blue mold is the vernacular name of a common postharvest disease of stored apples, pears, and quince that is caused by several common species of Penicillium . This study reports the draft genome sequence of Penicillium expansum strain R21, which was isolated from a red delicious apple in 2011 in Pennsylvania.

Penicillium spp. has been genetically manipulated and gene function studies have utilized single gene deletion strains for phenotypic analysis. Fungal transformation experiments have relied on hygromycin and hygromycin phosphotransferase (hph) as the main dominant selectable marker (DSM) system in Penicillium spp. This poses a limitation on the number of loci that can be analyzed and complemented in reverse genetic studies. Additionally, many economically important Penicillium spp. have not been evaluated to determine the utility of additional chemicals that can serve as DSMs. Therefore, six compounds were examined for 15 blue mold strains and their Minimum Inhibitory Concentrations (MICs) determined. Phleomycin, neomycin and G418 were deemed ineffective, as Penicillium spp. growth was observed on media amended with 1000 μg/ml of each compound. The efficacy of bialophos to inhibit fungal growth was intermediate, with MICs ranging from 250 to 1000 μg/ml and was species-dependent. However, chlorimuron ethyl and benlate had the lowest MIC values and minimal variation in efficacy within and between species. Therefore, benlate and chlorimuron ethyl are good candidates for use as since corresponding fungal resistance genes have been cloned, characterized and are available from a variety of public and academic sources.

Aspergillus flavus produces potent mutagenic and carcinogenic polyketide-derived secondary metabolites known as aflatoxins. Development of host plant resistance in peanut and other crops is the most environmentally friendly and cost-effective method to eliminate the serious problem of aflatoxin contamination in grains. To confirm that putative peanut genes identified in a previous microarray study were involved in peanut resistance to A. flavus infection, 14 genes were selected for further investigation through real-time PCR. The results revealed diverse patterns of gene expression during seed germination after A. flavus inoculation. Based on the expression levels and the relative-expression patterns over a 7-day period, the 14 host genes could be classified into six different groups belonging to three main biochemical and genetic defence processes of lipid metabolism, oxidative signalling and cell-wall synthesis during counter-attack. A network of gene expression patterns was activated in sequential order in response to A. flavus invasion in both resistant and susceptible peanut lines during seed germination. Understanding gene expression patterns in peanut will be useful to breeders and other scientists interested in incorporating genetic resources of resistance against A. flavus into peanut germplasm and/or commercial cultivars via conventional and/or molecular methods.

Botrytis cinerea causes gray mold and is an economically important postharvest pathogen of fruit, vegetables, and ornamentals. Fludioxonil-sensitive B. cinerea isolates were collected in 2011 and 2013 from commercial storage in Pennsylvania. Eight isolates had values for effective concentrations for inhibiting 50% of mycelial growth of 0.0004 to 0.0038 μg/ml for fludioxonil and were dual resistant to pyrimethanil and thiabendazole. Resistance was generated in vitro, following exposure to a sublethal dose of fludioxonil, in seven of eight dual-resistant B. cinerea isolates. Three vigorously growing B. cinerea isolates with multiresistance to postharvest fungicides were further characterized and found to be osmosensitive and retained resistance in the absence of selection pressure. A representative multiresistant B. cinerea strain caused decay on apple fruit treated with postharvest fungicides, which confirmed the in vitro results. The R632I mutation in the Mrr1 gene, associated with fludioxonil resistance in B. cinerea, was not detected in multipostharvest fungicide-resistant B. cinerea isolates, suggesting that the fungus may be using additional mechanisms to mediate resistance. Results from this study show for the first time that B. cinerea with dual resistance to pyrimethanil and thiabendazole can also rapidly develop resistance to fludioxonil, which may pose control challenges in the packinghouse environment and during long-term storage.

Penicillium solitum is one of the most prevalent species causing postharvest decay of pomaceous fruits during storage. Here, we report the draft genome of P. solitum strain NJ1, received as a transfer of a strain originally identified as P. griseofulvum by classical means.

Aflatoxin contamination caused by Aspergillus flavus infection of corn is a significant and chronic threat to corn being used as food or feed. Contamination of crops at levels of 20 ng g(-1) or higher (as regulated by the USFDA) by this toxin and potent carcinogen makes the crop unsalable, resulting in a significant economic burden on the producer. This review focuses on elimination of this contamination in corn which is a major US crop and the basis of many products. Corn is also "nature's example" of a crop containing heritable resistance to aflatoxin contamination, thereby serving as a model for achieving resistance to aflatoxin contamination in other crops as well. This crop is the largest production grain crop worldwide, providing food for billions of people and livestock and critical feedstock for production of biofuels. In 2011, the economic value of the US corn crop was US$76 billion, with US growers producing an estimated 12 billion bushels, more than one-third of the world's supply. Thus, the economics and significance of corn as a food crop and the threat to food safety due to aflatoxin contamination of this major food crop have prompted the many research efforts in many parts of the world to identify resistance in corn to aflatoxin contamination. Plant breeding and varietal selection has been used as a tool to develop varieties resistance to disease. This methodology has been employed in defining a few corn lines that show resistance to A. flavus invasion; however, no commercial lines have been marketed. With the new tools of proteomics and genomics, identification of resistance mechanisms, and rapid resistance marker selection methodologies, there is an increasing possibility of finding significant resistance in corn, and in understanding the mechanism of this resistance.

In order to utilize germplasm resources more efficiently for peanut (Arachis hypogaea L.) genetic improvement, a core collection of 576 accessions and a primary mini core collection of 298 accessions were developed previously from a collection of 6839 cultivated peanut lines stored at the Oil Crops Research Institute of Chinese Academy of Agricultural Sciences at Wuhan. For an efficient evaluation and characterization of the most useful agronomic and disease-resistant traits, an even smaller collection of peanut accessions that represent a spectrum of phenotypes could be more desirable. For this reason, a mini-mini core collection with 99 accessions from the core accessions was developed based on the analysis of 21 morphological traits. It was demonstrated that there were no significant differences between the core and mini-mini core collections in 20 out of the 21 morphological traits studied. Further, the mini-mini core collection captured the ranges of all of the 21 traits displayed in the core collection. The newly developed mini-mini core collection was assessed for resistance to bacterial wilt disease caused by Ralstonia solanacearum. Two accessions showing a high level of resistance to bacterial wilt were identified, demonstrating the usefulness of the mini-mini core collection. The mini-mini-core collection provides a more efficient means of germplasm evaluation and will be resequenced as part of the International Peanut Genome Consortium sequencing project at the UC-Davis Genome Center.

Response surface methodology was employed to optimize the degradation conditions of AFB1 by Rhodococcus erythropolis in liquid culture. The most important factors that influence the degradation, as identified by a two-level Plackett-Burman design with six variables, were temperature, pH, liquid volume, inoculum size, agitation speed and incubation time. Central composite design (CCD) and response surface analysis were used to further investigate the interactions between these variables and to optimize the degradation efficiency of R. erythropolis based on a second-order model. The results demonstrated that the optimal parameters were: temperature, 23.2 °C, pH, 7.17, liquid volume, 24.6 mL in 100-mL flask, inoculum size, 10%, agitation speed, 180 rpm, and incubation time, 81.9 h. Under these conditions, the degradation efficiency of R. erythropolis could reach 95.8% in liquid culture, which was increased by about three times as compared to non-optimized conditions. The result by mathematic modeling has great potential for aflatoxin removal in industrial fermentation such as in food processing and ethanol production.

Penicillium species cause postharvest decay, commonly known as blue mold, in pome fruits, such as apples and pears. To devise novel strategies to prevent and reduce economic losses during storage, the genome sequence of Penicillium solitum RS1 is reported here for the first time.

With 9 figures and 1 table Abstract Over the past five decades, cultivated peanut in China has been subjected to strong artificial selection in breeding programmes. To investigate the impact of artificial selection on expression diversity, we compared gene expression profiles in pod and leaf of five widespread cultivars in Southern China. In terms of tissues, hierarchical clustering analysis revealed that expression data of pod and leaf generated different dendrograms owing to artificial selection. K-means analysis also showed that there were 16 gene expression patterns in leaf, while only eight in pod. In considering cultivars, a cultivar specificity index (τ) was employed to characterize expression patterns, which suggested that genes having 0.15 80% of all expression patterns. Additionally, the diversity of gene expression in pod among cultivars of the ‘YY7’ pedigree decreased from 23.8% to 3.9%. Taken together, nucleotide polymorphisms in regulatory elements owing to artificial selection led to low-expression polymorphisms in both tissues and cultivars, contributed to the narrow genetic diversity and might be a driving force behind the breeding of cultivated peanut.

Aflatoxins are carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and Aspergillus parasiticus. Previous studies found that repeated serial mycelial transfer or treatment of A. parasiticus with 5-azacytidine produced colonies with a fluffy phenotype and inability to produce aflatoxins. To understand how these treatments affect expression of genes involved in aflatoxin production and development, we carried out expressed sequence tag (EST)-based microarray assays to identify genes in treated clones that are differentially expressed compared to the wild-type. Expression of 183 genes was significantly dysregulated. Of these, 38 had at least two-fold or lower expression compared to the untreated control and only two had two-fold or higher expression. The most frequent change was downregulation of genes predicted to encode membrane-bound proteins. Based on this result we hypothesize that the treatments cause changes in the structure of cellular and organelle membranes that prevent normal development and aflatoxin biosynthesis.

To better understand the effect of temperature on mycotoxin biosynthesis, RNA-Seq technology was used to profile the Aspergillus flavus transcriptome under different temperature conditions. This approach allowed us to quantify transcript abundance for over 80% of fungal genes including 1153 genes that were differentially expressed at 30 and 37 °C. Eleven of the 55 secondary metabolite clusters were upregulated at the lower temperature, including aflatoxin biosynthesis genes, which were among the most highly upexpressed genes. On average, transcript abundance for the 30 aflatoxin biosynthesis genes was 3300 times greater at 30 °C as compared with 37 °C. The results are consistent with the view that high temperature negatively affects aflatoxin production by turning down transcription of the two key transcriptional regulators, aflR and aflS. Subtle changes in the expression levels of aflS to aflR appear to control transcription activation of the aflatoxin cluster.

Genes encoding for glycosyl hydrolases (GH) in multiple families were recovered from an expression sequence tag library of Coptotermes formosanus, a xylophagous lower termite species. Functional analyses of these genes not only shed light on the mechanisms the insect employs to successfully use cellulosic materials as energy sources, which may serve as strategic targets for designing molecular-based bio-pesticides, but also enrich discoveries of new cellulolytic enzymes for conversion of biomass into biofuel. Our study demonstrated that cellulose could be converted to glucose by two recombinant endogenous glycosyl hydrolases (endo-β-1,4 glucanase in GH9 and β-glucosidase in GH1). While the former cleaved cellulose to cellobiose and cellotriose, the resulting simple cellodextrins were digested to glucose. Both of the Escherichia coli-expressed recombinant proteins showed properties that could be incorporated in a glucose-based ethanol production program.

SUMMARY Species of Aspergillus produce a diverse array of secondary metabolites, and recent genomic analysis has predicted that these species have the capacity to synthesize many more compounds. It has been possible to infer the presence of 55 gene clusters associated with secondary metabolism in Aspergillus flavus; however, only three metabolic pathways—aflatoxin, cyclopiazonic acid (CPA) and aflatrem—have been assigned to these clusters. To gain an insight into the regulation of and to infer the ecological significance of the 55 secondary metabolite gene clusters predicted in A. flavus, we examined their expression over 28 diverse conditions. Variables included culture medium and temperature, fungal development, colonization of developing maize seeds and misexpression of laeA, a global regulator of secondary metabolism. Hierarchical clustering analysis of expression profiles allowed us to categorize the gene clusters into four distinct clades. Gene clusters for the production of aflatoxins, CPA and seven other unknown compound(s) were identified as belonging to one clade. To further explore the relationships found by gene expression analysis, aflatoxin and CPA production were quantified under five different cell culture environments known to be conducive or nonconducive for aflatoxin biosynthesis and during the colonization of developing maize seeds. Results from these studies showed that secondary metabolism gene clusters have distinctive gene expression profiles. Aflatoxin and CPA were found to have unique regulation, but are sufficiently similar that they would be expected to co-occur in substrates colonized with A. flavus.

Mycotoxins are fungal metabolites that can contaminate food and feed crops worldwide and are responsible for toxic effects in animals and humans that consume contaminated commodities. Regulatory guidelines and limits for mycotoxins have been set by the US Food and Drug Administration (FDA) and food safety agencies of other countries for both import and export of affected commodities. Mycotoxin contamination of foods and feeds can also cause serious economic hardships to producers, processors, and the consumer. Therefore, there has been a concerted effort by researchers worldwide to develop strategies for the effective control of mycotoxin contamination of crops, particularly at the pre-harvest stage. Strategies currently being utilised to combat pre-harvest mycotoxin contamination include: (1) use of non-toxigenic biocontrol strains; (2) improved agricultural practices; (3) application of agrochemicals; (4) plant breeding for resistance; and (5) genetic engineering of resistance genes into crop plants. This article highlights research on the genetic engineering of plants for resistance to invasion by mycotoxigenic fungi as well as detoxification of mycotoxins. Emphasis is placed on the most economically relevant fungi and the mycotoxins they produce. These include aflatoxins produced mainly by Aspergillus flavus and A. parasiticus, trichothecenes produced mainly by Fusarium graminearum, and to a lesser extent, fumonisins produced by F. verticillioides. Information is also presented on the use of genomics and proteomics technologies as a means of identifying genes and proteins that can be utilised in transgenic approaches to control the growth of mycotoxigenic fungi and the mycotoxins that they produce in food and feed crops.

We have examined the feasibility of using array comparative genomic hybridization (aCGH) to explore intraspecific genetic variability at the genomic level in two pathogenic molds, Aspergillus fumigatus and Aspergillus flavus. Our analysis showed that strain-specific genes may comprise up to 2% of their genomes in comparison to isolates from different vegetative (heterokaryon) compatibility groups (VCGs). In contrast, isolates with the same VCG affiliations have almost identical gene content. Most isolate-specific genes are annotated as 'hypothetical' and located in a few large subtelomeric indels. The list includes highly polymorphic loci that contain putative het (heterokaryon compatibility) loci, which determine the individual's VCG during parasexual crossing. Incidentally, VCGs in both species seem to be significantly associated with either alpha or HMG mating type (Chi-square test, P=0.05). In conclusion CGH can be used to effectively to identify isolate-specific genes in Aspergillus species. Preliminary evidence suggests that gene flow in both species is largely constrained by VCG boundaries, although further VCG sampling is required to confirm this observation.

Peanut (Arachis hypogaea L.), or groundnut, is an important crop economically and nutritionally in many tropical and subtropical areas of the world. It is also one of the most susceptible host crops to Aspergillus flavus resulting in aflatoxin contamination. The prevention or elimination of aflatoxin contamination in preharvest and postharvest crops is a serious challenge facing scientists. The recent International Conference on Groundnut Aflatoxin Management and Genomics held in Guangzhou, China, provided an international forum for discussions on the latest accomplishments, the development of strategies, and the initiation of cooperative research for the prevention of aflatoxin contamination. This review summarizes the progress in genetic and genomic research of peanuts and the toxin-producing fungus A. flavus. In particular, the pathway for production and the genetic regulation of afaltoxin, and the peanut-Aspergillus interaction are discussed. The use of a peanut-Aspergillus microarray will help scientists to study the crop-pathogen interaction; aids in the identification of genes involved in both fungal invasion and crop resistance, and ultimately enhance research to find solutions that prevent aflatoxin contamination in agricultural commodities.

Aspergillus oryzae has been used in Japanese fermentation industries for more than a thousand years. The species produces large amounts of various hydrolytic enzymes and has been successfully applied to modern biotechnology. The size of the A. oryzae genome (37.5 Mb) is very close to that of A. flavus and A. niger, and 20-30% larger than that of either A. nidulans or A. fumigatus. A. oryzae and A. flavus have exactly the same number of aspartic proteinase genes, of which each orthologous pair shares highly conserved amino acid sequences. Synteny analysis with A. fumigatus and A. nidulans showed that the A. oryzae genome has a mosaic structure consisting of syntenic and non-syntenic blocks. In the microorganisms to be compared, the density of the genes having homologs was obviously higher on the syntenic than on the non-syntenic blocks. Expression analysis by the DNA microarray supported the significantly lower expression of genes on the non-syntenic than on the syntenic blocks.

Aflatoxins are highly carcinogenic secondary metabolites produced primarily by the fungi Aspergillus flavus and Aspergillus parasiticus. Aflatoxin contamination of food and feed is an age old problem of particular concern over the last four decades. Now, for the first time control measures for this problem appear within reach. For practical and sustainable control of aflatoxin contamination to be realised, however, additional information is needed rather rapidly, particularly for understanding the specific molecular factors (both in the plant and the fungus) involved during host plant-fungus interaction. The information derived from the use of novel tools such as genomics, proteomics and metabolomics provides us with the best and the quickest opportunity to achieve a clear understanding of the survival of toxigenic fungi in the field, the ability of the fungus to invade crops, and the process of toxin contamination under various environmental conditions. Significant progress has been made recently in understanding the genomic makeup of the most significant aflatoxin producing field fungus, namely Aspergillus flavus. Progress also has been made in the study of host crop resistance to fungal invasion through the use of proteomics. The information available on production of aflatoxin and other metabolites by Aspergillus flavus is reasonably extensive, although the application of metabolomics as a tool in this study is relatively new. In this review there is a discussion of the use of genomics, proteomics and metabolomics in deriving the requisite information for developing effective strategies to interrupt the machinery in the fungus for production of these toxins, as well as to assist in the development of host-resistance against fungal invasion and aflatoxin contamination of crops.

Aflatoxins are carcinogenic fungal secondary metabolites produced by Aspergillus flavus and other closely related species. Levels of aflatoxins in agricultural commodities are stringently regulated by many countries because of the health hazard, and thus, aflatoxins are of major concern to both producers and consumers. A cluster of genes responsible for aflatoxin biosynthesis has been identified; however, expression of these genes is a complex and poorly understood phenomenon. To better understand the molecular events that are associated with aflatoxin production, three separate nonaflatoxigenic A. flavus strains were produced through serial transfers of aflatoxigenic parental strains. The three independent aflatoxigenic/nonaflatoxigenic pairs were compared via transcription profiling by microarray analyses. Cross comparisons identified 22 features in common between the aflatoxigenic/nonaflatoxigenic pairs. Physical mapping of the 22 features using the Aspergillus oryzae genome sequence for reference identified 16 unique genes. Aflatoxin biosynthetic and regulatory gene expression levels were not significantly different between the aflatoxigenic/nonaflatoxigenic pairs, which suggests that the inability to produce aflatoxins is not due to decreased expression of known biosynthetic or regulatory genes. Of the 16 in common genes, only one gene homologous to glutathione S-transferase genes showed higher expression in the nonaflatoxigenic progeny relative to the parental strains. This gene, named hcc, was selected for over-expression in an aflatoxigenic A. flavus strain to determine if it was directly responsible for loss of aflatoxin production. Although hcc transformants showed six- to ninefold increase in expression, no discernible changes in colony morphology or aflatoxin production were detected. Possible roles of hcc and other identified genes are discussed in relation to regulation of aflatoxin biosynthesis.

Aflatoxins are toxic and carcinogenic polyketide metabolites produced by fungal species, including Aspergillus flavus and A. parasiticus. The biosynthesis of aflatoxins is modulated by many environmental factors, including the availability of a carbon source. The gene expression profile of A. parasiticus was evaluated during a shift from a medium with low concentration of simple sugars, yeast extract (YE), to a similar medium with sucrose, yeast extract sucrose (YES). Gene expression and aflatoxins (B1, B2, G1, and G2) were quantified from fungal mycelia harvested pre- and post-shifting. When compared with YE media, YES caused temporary reduction of the aflatoxin levels detected at 3-h post-shifting and they remained low well past 12 h post-shift. Aflatoxin levels did not exceed the levels in YE until 24 h post-shift, at which time point a tenfold increase was observed over YE. Microarray analysis comparing the RNA samples from the 48-h YE culture to the YES samples identified a total of 2120 genes that were expressed across all experiments, including most of the aflatoxin biosynthesis genes. One-way analysis of variance (ANOVA) identified 56 genes that were expressed with significant variation across all time points. Three genes responsible for converting norsolorinic acid to averantin were identified among these significantly expressed genes. The potential involvement of these genes in the regulation of aflatoxin biosynthesis is discussed.

Aspergillus section Flavi includes aflatoxin-producing and nonproducing fungi. Aspergillus sojae is unable to produce aflatoxins and is generally recognized as safe for food fermentation. However, because of its taxonomical relatedness to aflatoxin-producing Aspergillus parasiticus and A. flavus, it is necessary to decipher the underlying mechanisms for its inability to produce aflatoxins. This review addresses the relationship between A. sojae and A. parasiticus and the advances that have been made in aflatoxin biosynthesis research, especially with regard to gene structure, genome organization, and gene regulation in A. parasiticus and A. flavus and how this has been used to assure the safety of A. sojae as an organism for food fermentation. The lack of aflatoxin-producing ability of A. sojae results primarily from an early termination point mutation in the pathway-specific aflR regulatory gene, which causes the truncation of the transcriptional activation domain of AflR and the abolishment of interaction between AflR and the AflJ co-activator. Both are required for gene expression. In addition, a defect in the polyketide synthase gene also contributes to its nonaflatoxigenicity.

Species of Aspergillus section Flavi were isolated and identified in maize samples collected from a wide geographical region in northeastern China. Aspergillus flavus was identified to be the primary species in the population (99%) becoming a potential source of aflatoxin contamination in the region. Isolated A. flavus strains were classified into the S and L strains respectively based on their sclerotia morphology. Among the A. flavus strains identified, L strains dominated over the S strains in the maize samples studied. Both uniseriate and biseriate forms were observed in A. flavus L strain isolates. However, only uniseriate was observed in A. flavus S strain isolates. Microscopic characteristics of L and S strains were observed and reported. Some geographical differences between northeastern China and other countries and regions were discussed. This is the first study on the population dynamics of A. flavus versus A. parasiticus and the L and S strains within A. flavus in maize samples in northeastern China.

Aflatoxins are toxic and carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and Aspergillus parasiticus. To better understand the molecular mechanisms that regulate aflatoxin production, the biosynthesis of the toxin in A. flavus and A. parasticus grown in yeast extract sucrose media supplemented with 50 mM tryptophan (Trp) were examined. Aspergillus flavus grown in the presence of 50 mM tryptophan was found to have significantly reduced aflatoxin B(1) and B(2) biosynthesis, while A. parasiticus cultures had significantly increased B(1) and G(1) biosynthesis. Microarray analysis of RNA extracted from fungi grown under these conditions revealed 77 genes that are expressed significantly different between A. flavus and A. parasiticus, including the aflatoxin biosynthetic genes aflD (nor-1), aflE (norA), and aflO (omtB). It is clear that the regulatory mechanisms of aflatoxin biosynthesis in response to Trp in A. flavus and A. parasiticus are different. These candidate genes may serve as regulatory factors of aflatoxin biosynthesis.